Soil metagenomics, the study of the collective genomes of soil microorganisms, addresses limitations in traditional culture-dependent methods by using culture-independent sequencing technologies. This field directly investigates microbial diversity, functional activities, and community structure in soil settings using methods including shotgun sequencing and high-throughput sequencing. To learn more about the roles that the soil microbiome plays in nutrient cycle and soil health, the procedure includes DNA extraction, sequencing, data processing, taxonomic classification, and functional annotation. Its uses in agriculture have revolutionized the field, especially in improving biological nitrogen fixation by targeted microbial insights and increasing crop output by controlling biotic stress. These advances support sustainable farming practices and promote soil health.